Whole Genome Sequencing Analysis of Nontyphoidal Salmonella enterica of Chicken Meat and Human Origin Under Surveillance in Sri Lanka

Research output: Contribution to journalJournal article – Annual report year: 2019Researchpeer-review



  • Author: Tay, Moon Y F

    Nanyang Technological University, Singapore

  • Author: Pathirage, Sujatha

    Medical Research Institute (MRI), Sri Lanka

  • Author: Chandrasekaran, Lakshmi

    Nanyang Technological University, Singapore

  • Author: Wickramasuriya, Uddami

    Medical Research Institute (MRI), Sri Lanka

  • Author: Sadeepanie, Nirasha

    Medical Research Institute (MRI), Sri Lanka

  • Author: Waidyarathna, Kaushalya D K

    Medical Research Institute (MRI), Sri Lanka

  • Author: Liyanage, Liyanaralalage Dilini Chathurika

    Medical Research Institute (MRI), Sri Lanka

  • Author: Seow, Kelyn L G

    Nanyang Technological University, Singapore

  • Author: Hendriksen, Rene S.

    Research group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Takeuchi, Masami T

    Food and Agriculture Organization of the United Nations, Italy

  • Author: Schlundt, Jørgen

    Nanyang Technological University, Singapore

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A total of 73 nontyphoidal Salmonella enterica isolates, 33 from raw chicken meat and 40 from routine clinical specimens, were collected between 2015 and 2017 from eight cities in Sri Lanka for a pilot study of whole genome sequencing for Salmonella surveillance. The isolates were characterized by conventional serotyping and whole genome sequencing. The raw sequenced data were assembled and analyzed to predict Salmonella serotypes, determine sequence type (ST) profiles of genome and plasmid, and identify plasmid replicon sequences and antimicrobial resistance (AMR) genes. The most common serovar isolated from chicken meat was Salmonella enterica serovar Agona of ST13 (n = 16), in contrast to Salmonella enterica serovar Enteritidis of ST11 (n = 21) in human. Salmonella enterica serovar Corvallis is the only serovar that was overlapping between human and chicken meat. The level of agreement between serotyping and serotype prediction results was 100%. Among the 33 chicken isolates, multidrug resistance (MDR) was observed in five isolates, including two Salmonella enterica serovar Kentucky ST314, which harbored six different classes of AMR determinants. Among the 40 human isolates, MDR was detected in two Salmonella enterica serovar Chester (ST2063) isolates containing five different antibiotic classes of AMR determinants. Out of 73 isolates, the only human Salmonella enterica serovar Typhimurium strain of ST36 was found to possess extended-spectrum beta-lactamase (ESBL) gene, blaCTX-M-15, and it was positive for ESBL production. In summary, this study identified S. enterica serovars that were dominating in chicken meat and human and showed the genomic differences among the chicken meat and human strains. It should be noted that the limited number of isolates and sampling at a different time period means that thorough source attribution is not possible. To the best of our knowledge, this is the first report on the use of whole genome sequencing analysis of nontyphoidal S. enterica isolated from chicken meat and human in Sri Lanka.
Original languageEnglish
JournalFoodborne pathogens and disease
Issue number7
Number of pages7
Publication statusPublished - 2019
CitationsWeb of Science® Times Cited: No match on DOI

    Research areas

  • CTX-M-15, Sri Lanka, Chicken meat, Human, Surveillance, Whole genome sequencing, Salmonella enterica

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